Not sure if you got this fixed, but I this issue and finally figured out - so I wanted to share what I did, in hopes it helps anyone else who Googles this topic.
Basically, I was missing about 100GB of space on my SSD. Disk Utility, Get Info, and DaisyDisk were all telling me different answers about how much disk space I had on my 256GB SSD (2013 Mac Book Air running Yosemite). I only had about 90GB used, but instead of having roughly 160GB available, everything was telling me I had only 59-70GB left. I knew this was way wrong.
I tried Repair in Disk Utility, disabling and re-enabling Time Machine, re-booting, and a bunch of other stuff I read online that might help. Nothing did.
What *finally* worked - luckily I had some cheap old USB drives around to make this possible:
1) Backed up my important files to an external drive in case this all failed, and I had to "nuke and pave" everything. Disconnected that drive and set it aside.
2) Connected a different empty external drive, and made a bootable backup of my MacBook Air's SSD with SuperDuper (I expect Carbon Copy Cloner would work too). Takes a while - watch a baseball game or something, and come back later.
3) After that was made, I kept that drive connected, and in System Preferences I set that as the Startup Disk, then rebooted into that drive.
4) Now when I booted up from the external drive, I ran Repair in Disk Utility on the MacBook Air's SSD.
Something about running Disk Utility from the external drive must have made a difference, because it found a bunch of weird things and fixed them.
5) Once done, go to System Preferences, set Startup Disk back to the SSD again.
6) Reboot
And, voila, there was my 100GB back again.
Your mileage may vary, and of course backup twice before you try this... but it worked for me. Best of luck!